Literature DB >> 34153213

Molecular Epigenetics: Chemical Biology Tools Come of Age.

John D Bagert1, Tom W Muir1.   

Abstract

The field of epigenetics has exploded over the last two decades, revealing an astonishing level of complexity in the way genetic information is stored and accessed in eukaryotes. This expansion of knowledge, which is very much ongoing, has been made possible by the availability of evermore sensitive and precise molecular tools. This review focuses on the increasingly important role that chemistry plays in this burgeoning field. In an effort to make these contributions more accessible to the nonspecialist, we group available chemical approaches into those that allow the covalent structure of the protein and DNA components of chromatin to be manipulated, those that allow the activity of myriad factors that act on chromatin to be controlled, and those that allow the covalent structure and folding of chromatin to be characterized. The application of these tools is illustrated through a series of case studies that highlight how the molecular precision afforded by chemistry is being used to establish causal biochemical relationships at the heart of epigenetic regulation.

Entities:  

Keywords:  chemical biology; chemical tools; chromatin; epigenetics

Mesh:

Substances:

Year:  2021        PMID: 34153213      PMCID: PMC8284505          DOI: 10.1146/annurev-biochem-080120-021109

Source DB:  PubMed          Journal:  Annu Rev Biochem        ISSN: 0066-4154            Impact factor:   27.258


  199 in total

1.  Enzymatic Synthesis of Base-Functionalized Nucleic Acids for Sensing, Cross-linking, and Modulation of Protein-DNA Binding and Transcription.

Authors:  Michal Hocek
Journal:  Acc Chem Res       Date:  2019-06-05       Impact factor: 22.384

2.  Labeling substrates of protein arginine methyltransferase with engineered enzymes and matched S-adenosyl-L-methionine analogues.

Authors:  Rui Wang; Weihong Zheng; Haiqiang Yu; Haiteng Deng; Minkui Luo
Journal:  J Am Chem Soc       Date:  2011-05-03       Impact factor: 15.419

3.  Se-adenosyl-L-selenomethionine cofactor analogue as a reporter of protein methylation.

Authors:  Ian R Bothwell; Kabirul Islam; Yuling Chen; Weihong Zheng; Gil Blum; Haiteng Deng; Minkui Luo
Journal:  J Am Chem Soc       Date:  2012-09-04       Impact factor: 15.419

Review 4.  Comprehensive Catalog of Currently Documented Histone Modifications.

Authors:  Yingming Zhao; Benjamin A Garcia
Journal:  Cold Spring Harb Perspect Biol       Date:  2015-09-01       Impact factor: 10.005

5.  Super-resolution Imaging of Individual Human Subchromosomal Regions in Situ Reveals Nanoscopic Building Blocks of Higher-Order Structure.

Authors:  Ke Fang; Xuecheng Chen; Xiaowei Li; Yi Shen; Jielin Sun; Daniel M Czajkowsky; Zhifeng Shao
Journal:  ACS Nano       Date:  2018-05-04       Impact factor: 15.881

6.  Nucleosome accessibility governed by the dimer/tetramer interface.

Authors:  Vera Böhm; Aaron R Hieb; Andrew J Andrews; Alexander Gansen; Andrea Rocker; Katalin Tóth; Karolin Luger; Jörg Langowski
Journal:  Nucleic Acids Res       Date:  2010-12-21       Impact factor: 16.971

7.  Phase transitions in the assembly of multivalent signalling proteins.

Authors:  Pilong Li; Sudeep Banjade; Hui-Chun Cheng; Soyeon Kim; Baoyu Chen; Liang Guo; Marc Llaguno; Javoris V Hollingsworth; David S King; Salman F Banani; Paul S Russo; Qiu-Xing Jiang; B Tracy Nixon; Michael K Rosen
Journal:  Nature       Date:  2012-03-07       Impact factor: 49.962

8.  5-Hydroxymethylcytosine signatures in circulating cell-free DNA as diagnostic biomarkers for human cancers.

Authors:  Wenshuai Li; Xu Zhang; Xingyu Lu; Lei You; Yanqun Song; Zhongguang Luo; Jun Zhang; Ji Nie; Wanwei Zheng; Diannan Xu; Yaping Wang; Yuanqiang Dong; Shulin Yu; Jun Hong; Jianping Shi; Hankun Hao; Fen Luo; Luchun Hua; Peng Wang; Xiaoping Qian; Fang Yuan; Lianhuan Wei; Ming Cui; Taiping Zhang; Quan Liao; Menghua Dai; Ziwen Liu; Ge Chen; Katherine Meckel; Sarbani Adhikari; Guifang Jia; Marc B Bissonnette; Xinxiang Zhang; Yupei Zhao; Wei Zhang; Chuan He; Jie Liu
Journal:  Cell Res       Date:  2017-09-19       Impact factor: 25.617

9.  Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping.

Authors:  Stefanie L Morgan; Natasha C Mariano; Abel Bermudez; Nicole L Arruda; Fangting Wu; Yunhai Luo; Gautam Shankar; Lin Jia; Huiling Chen; Ji-Fan Hu; Andrew R Hoffman; Chiao-Chain Huang; Sharon J Pitteri; Kevin C Wang
Journal:  Nat Commun       Date:  2017-07-13       Impact factor: 14.919

10.  Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins.

Authors:  Morgan L Maeder; James F Angstman; Marcy E Richardson; Samantha J Linder; Vincent M Cascio; Shengdar Q Tsai; Quan H Ho; Jeffry D Sander; Deepak Reyon; Bradley E Bernstein; Joseph F Costello; Miles F Wilkinson; J Keith Joung
Journal:  Nat Biotechnol       Date:  2013-10-09       Impact factor: 54.908

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  2 in total

1.  A Genetically Encoded Approach for Breaking Chromatin Symmetry.

Authors:  Bradley J Lukasak; Robert E Thompson; Michelle M Mitchener; Vanessa J Feng; John D Bagert; Tom W Muir
Journal:  ACS Cent Sci       Date:  2022-02-01       Impact factor: 18.728

2.  Editorial: Epigenetics of the immune component of inflammation.

Authors:  Yan-Jun Liu; Haitao Wang; Hai-Jing Zhong; Cheong-Meng Chong; Guan-Jun Yang
Journal:  Front Immunol       Date:  2022-08-22       Impact factor: 8.786

  2 in total

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